Comparative performance of AmpFLSTR® Identifiler® Plus PCR amplification kit and QIAGEN® Investigator® IDplex Plus kit.

Many forensic STR kits are currently available in the market. The AmpFLSTR® Identifiler® Plus kit, which targets 15 STRs, is commonly used worldwide. The Thai forensic DNA community is built around it in terms of instrument, databases, and interpretation. QIAGEN's IDplex Plus kit targets the same loci, but the PCR cycling time is shorter by about 90min. A direct comparison that assesses forensic parameters and applicability to casework between the two kits has never been carried out. In this study, we performed a direct comparison between the two kits using serial dilutions of two control DNA samples and 60 randomly selected casework samples, including samples taken from improvised explosive devices and terrorist raids. We statistically compared the performance of the two kits in terms of peak height, number of allele detected (allelic drop-out), intra-locus balance, inter-locus balance, inhibitor tolerance, stutter ratio, concordance, and allelic drop-in. The results demonstrate that both kits are statistically similar in performance. IDplex Plus gave higher peak heights in sensitivity test and tolerated inhibitors better, but had slightly worse inter-locus balances and stutter ratios. However, these differences were not practically significant, as seen by the resulting profiles of the casework samples (p=0.601). The performance on low-template samples also was not different. In conclusion, laboratories looking to replace the aging Identifiler® Plus might consider the IDplex Plus as a faster, more robust alternative that fits right into their existing structure without further investment in instrument and DNA database. Having more kits available worldwide by different companies could help bring the technology to different forensic laboratories and the justice system as a whole.

Forensic STR loci reveal common genetic ancestry of the Thai-Malay Muslims and Thai Buddhists in the deep Southern region of Thailand.

Among the people living in the five deep Southern Thai provinces, Thai-Malay Muslims (MUS) constitute the majority, while the remaining are Thai Buddhists (BUD). Cultural, linguistic and religious differences between these two populations have been previously reported. However, their biological relationship has never been investigated. In this study, we aimed to reveal the genetic structure and genetic affinity between MUS and BUD by analyzing 15 autosomal short tandem repeats. Both distance and model-based clustering methods showed significant genetic homogeneity between these two populations, suggesting a common biological ancestry. After Islamization in this region during the fourteenth century AD, gradual albeit nonstatistically significant genetic changes occurred within these two populations. Cultural barriers possibly influenced these genetic changes. MUS have closer admixture to Malaysian-Malay Muslims than BUD countrywide. Admixture proportions also support certain degree of genetic dissimilarity between the two studied populations, as shown by the unequal genetic contribution from Malaysian-Malay Muslims. Cultural transformation and recent minor genetic admixture are the likely processes that shaped the genetic structure of both MUS and BUD.

Improved STR profiles from improvised explosive device (IED): fluorescence latent DNA detection and direct PCR.

Bombing accounts for the largest share of terrorist incidents worldwide. Most involve an improvised explosive device (IED): a bomb made from household items. Touch DNA may be left on parts of an IED during assembly. However, an IED conflagration degrades DNA, and there has never been a way to locate where touch DNA may remain. To solve this problem, we combined the use of fluorescent dye to locate latent DNA and direct PCR to improve STR profiles of DNA obtained from IEDs. Six fluorescent DNA-binding dyes were evaluated at various concentrations for the purpose of staining latent DNA. SYBR® Green I and Diamond™ Nucleic Acid dye were able to visualize touch DNA on IED substrates. Inhibition studies with extracted DNA and touch DNA using both dyes revealed that Diamond™ dye inhibited direct STR amplification, while SYBR® Green I did not. Stability studies at three temperatures showed optimum performance of SYBR® Green I up to 24 h after formulation. As such, only SYBR® Green I was further used to develop a "visualized-direct PCR" method. Using the conventional approach and the novel "visualized-direct PCR" approach in a single-blind investigation of mock IED evidence, the "visualized-direct PCR" approach had a 98.6% chance of obtaining more alleles (95% highest density interval (HDI): 0.7 to 10.0 alleles). A decrease in non-donor's alleles (mixed profiles) was also observed. The developed approach has the potential to revolutionize the process of STR typing from touch DNA.

Systematic study for DNA recovery and profiling from common IED substrates: From laboratory to casework.

Improvised explosive devices (IEDs) made from household items are encountered in terrorist attacks worldwide. Assembling an IED leaves trace DNA on its components, but deflagration degrades DNA. To maximize the amount of DNA recovered, a systematic evaluation of DNA collection methods was carried out and the most efficient methods were implemented with IED casework evidence as a validation exercise. Six swab types and six moistening agents were used to collect dried buffy coat stains on four common IED substrates. The most efficient swab/moistening agent combinations were then compared with tape-lifting using three brands of adhesive tape and also with direct DNA extraction from evidence. The most efficient collection methods for different IED substrates (post-study protocol) were then implemented for IED casework and compared with the pre-study protocol using 195 pieces of IED evidence. There was no single best swab type or moistening agent. Swab type had the largest effect on DNA recovery percentages, but moistening agents, substrates, and the interactions between factors all affected DNA recovery. The most efficient swab/moistening agent combinations performed equally well when compared with the best adhesive tape and direct extraction. The post-study protocol significantly improved STR profiles obtained from IED evidence. This paper outlines a comprehensive study of DNA collection methods for trace DNA and the validation of the most efficient collection methods with IED evidence. The findings from both parts of this study emphasize the need to continuously re-evaluate standard operating protocols with empirical studies.